Examining the stability of nucleosomal modifications during pull-down affinity purification

Here we investigated the stability of nucleosomal modifications during pull-down affinity purification with HeLa nuclear extracts. Unmodified di-nucleosomes and di-nucleosomes decorated with H3K4me3K9acK14acK18acK23acK27ac, H4K5acK8acK12acK16acK20me2 and incorporating histone variant H2A.Z were incubated with HeLa nuclear extract or buffer alone for 4 hours at 4 degrees Celsius. The relative abundances of nucleosomal modifications were quantified using LC-MS.